void setStateRecursive(RootedTree tree, PhyloNode base, int state) {
BreadthFirstIterator bfi = new BreadthFirstIterator(tree, base);
while (bfi.hasNext()) {
PhyloNode n = (PhyloNode) bfi.next();
n.setState(state);
}
}
void setPositionRecursive(RootedTree tree, PhyloNode base, PhyloNode positionToMe) {
BreadthFirstIterator bfi = new BreadthFirstIterator(tree, base);
while (bfi.hasNext()) {
PhyloNode n = (PhyloNode) bfi.next();
n.setPosition(positionToMe);
}
}
void clearCutNodes() {
if (origTree != null) {
if (origVertex != null && origVertex.getState() == PhyloNode.CUT) {
origTree.deleteSubtree(origVertex);
origTree.removeElbowsBelow(origTree.getRoot());
setStateRecursive(origTree, (PhyloNode) origTree.getRoot(), PhyloNode.NONE);
origVertex.found = false;
origVertex = null;
origTree.modPlus();
}
}
}
public synchronized void paste(CachedRootedTree destTree, PhyloNode destNode) {
// Translate the newick string into a RooteTree.
PhyloTree tree = loadClip();
// Add the clone's vertices and edges to the destination tree.
synchronized (destTree) {
destTree.setHoldCalculations(true);
Graphs.addGraph(destTree, tree);
// Insert the clone's root vertex into the midpoint above destNode.
if (destTree.getParentOf(destNode) == null) {
destTree.addEdge(destNode, tree.getRoot());
} else {
DefaultVertex internalVertex = destTree.createAndAddVertex();
((PhyloNode) internalVertex).setPosition(origVertex);
destTree.insertNodeBetween(destTree.getParentOf(destNode), destNode, internalVertex);
destTree.addEdge(internalVertex, tree.getRoot());
}
destTree.setHoldCalculations(false);
destTree.modPlus();
clearCutNodes();
}
}